Mercury in PDB 1mms: Crystal Structure of the Ribosomal Protein L11-Rna Complex

The structure of Crystal Structure of the Ribosomal Protein L11-Rna Complex, PDB code: 1mms was solved by B.T.Wimberly, R.Guymon, J.P.Mccutcheon, S.W.White, V.Ramakrishnan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.57
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.890, 84.260, 155.510, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 25.4

The structure of Crystal Structure of the Ribosomal Protein L11-Rna Complex also contains other interesting chemical elements:

Cadmium	(Cd)	8 atoms
Magnesium	(Mg)	19 atoms

The binding sites of Mercury atom in the Crystal Structure of the Ribosomal Protein L11-Rna Complex (pdb code 1mms). This binding sites where shown within 5.0 Angstroms radius around Mercury atom.
In total 8 binding sites of Mercury where determined in the Crystal Structure of the Ribosomal Protein L11-Rna Complex, PDB code: 1mms:
Jump to Mercury binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Mercury binding site 1 out of 8 in the Crystal Structure of the Ribosomal Protein L11-Rna Complex


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 1 of Crystal Structure of the Ribosomal Protein L11-Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Hg227 b:21.1 occ:0.10 N3 C:U1078 2.5 24.7 1.0 O2 C:U1078 3.0 29.6 1.0 OP1 C:G1089 3.0 30.8 1.0 C2 C:U1078 3.1 27.0 1.0 N6 C:A1077 3.4 32.9 1.0 C4 C:U1078 3.5 26.7 1.0 C5' C:G1089 3.6 29.5 1.0 O4 C:U1078 3.6 44.0 1.0 P C:G1089 4.2 26.5 1.0 O5' C:G1089 4.2 14.9 1.0 C6 C:A1077 4.3 29.0 1.0 N1 C:U1078 4.5 21.7 1.0 C3' C:A1088 4.6 27.8 1.0 C4' C:G1089 4.8 26.2 1.0 C5 C:U1078 4.8 18.5 1.0 O3' C:A1088 4.8 19.4 1.0 N1 C:A1077 5.0 23.4 1.0

Mercury binding site 2 out of 8 in the Crystal Structure of the Ribosomal Protein L11-Rna Complex


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 2 of Crystal Structure of the Ribosomal Protein L11-Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Hg230 b:65.0 occ:0.41 N3 C:U1061 2.2 73.7 1.0 O4 C:U1061 3.0 68.7 1.0 C4 C:U1061 3.0 67.1 1.0 C6 C:A1070 3.1 59.8 1.0 C2 C:U1061 3.2 62.3 1.0 N6 C:A1070 3.3 69.0 1.0 O2 C:U1061 3.3 62.3 1.0 C5 C:A1070 3.3 55.3 1.0 OP1 C:A1069 3.4 34.7 1.0 N1 C:A1070 3.6 56.3 1.0 N7 C:A1070 3.8 50.9 1.0 C4 C:A1070 4.0 46.6 1.0 C2 C:A1070 4.2 41.8 1.0 C5 C:U1061 4.4 54.5 1.0 N1 C:U1061 4.4 50.5 1.0 N3 C:A1070 4.5 44.2 1.0 C8 C:A1070 4.5 49.9 1.0 O3' C:G1068 4.6 40.5 1.0 P C:A1069 4.6 35.9 1.0 N9 C:A1070 4.7 42.7 1.0 C6 C:U1061 4.9 45.7 1.0

Mercury binding site 3 out of 8 in the Crystal Structure of the Ribosomal Protein L11-Rna Complex


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 3 of Crystal Structure of the Ribosomal Protein L11-Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Hg332 b:82.4 occ:0.60 N3 D:U1061 1.9 60.8 1.0 O4 D:U1061 2.6 48.6 1.0 C4 D:U1061 2.6 51.8 1.0 C2 D:U1061 3.0 53.5 1.0 C6 D:A1070 3.0 50.9 1.0 N6 D:A1070 3.2 62.3 1.0 C5 D:A1070 3.3 44.5 1.0 O2 D:U1061 3.3 44.6 1.0 N1 D:A1070 3.4 49.0 1.0 OP1 D:A1069 3.5 29.0 1.0 N7 D:A1070 3.8 45.9 1.0 C4 D:A1070 3.9 42.2 1.0 C5 D:U1061 4.0 40.8 1.0 C2 D:A1070 4.0 37.7 1.0 N1 D:U1061 4.2 45.0 1.0 N3 D:A1070 4.3 40.3 1.0 C8 D:A1070 4.5 43.8 1.0 C6 D:U1061 4.5 43.4 1.0 N9 D:A1070 4.6 42.6 1.0 P D:A1069 4.7 27.2 1.0 O3' D:G1068 4.8 38.7 1.0

Mercury binding site 4 out of 8 in the Crystal Structure of the Ribosomal Protein L11-Rna Complex


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 4 of Crystal Structure of the Ribosomal Protein L11-Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Hg347 b:54.2 occ:0.20 N3 D:U1078 2.5 28.6 1.0 O2 D:U1078 3.1 30.9 1.0 C2 D:U1078 3.2 35.3 1.0 OP1 D:G1089 3.2 28.3 1.0 O D:HOH346 3.4 40.4 1.0 C4 D:U1078 3.5 30.3 1.0 N6 D:A1077 3.6 25.1 1.0 C5' D:G1089 3.6 30.9 1.0 O4 D:U1078 3.6 39.1 1.0 O5' D:G1089 4.3 22.5 1.0 P D:G1089 4.4 27.7 1.0 C6 D:A1077 4.5 24.3 1.0 N1 D:U1078 4.6 25.9 1.0 C4' D:G1089 4.7 24.7 1.0 C3' D:A1088 4.8 28.6 1.0 C5 D:U1078 4.8 25.9 1.0 O3' D:A1088 5.0 22.0 1.0

Mercury binding site 5 out of 8 in the Crystal Structure of the Ribosomal Protein L11-Rna Complex


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 5 of Crystal Structure of the Ribosomal Protein L11-Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ D:Hg451 b:26.2 occ:0.10 N3 D:C1097 2.5 31.0 1.0 O2 D:C1097 2.6 29.2 1.0 C2 D:C1097 2.9 27.9 1.0 C4 D:C1097 3.6 45.0 1.0 N4 D:C1097 4.0 50.6 1.0 N1 D:C1097 4.3 31.4 1.0 O4' D:A1098 4.4 47.7 1.0 C1' D:A1098 4.5 36.9 1.0 N6 D:A1096 4.5 30.6 1.0 N1 D:A1096 4.6 23.8 1.0 C5 D:C1097 4.9 39.1 1.0 C6 D:A1096 4.9 23.5 1.0

Mercury binding site 6 out of 8 in the Crystal Structure of the Ribosomal Protein L11-Rna Complex


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 6 of Crystal Structure of the Ribosomal Protein L11-Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg415 b:35.2 occ:0.10 OG1 A:THR19 2.5 0.0 1.0 CB A:CYS39 2.6 93.9 1.0 C A:CYS39 3.7 96.3 1.0 CA A:CYS39 3.8 95.6 1.0 N A:LYS40 3.8 96.8 1.0 SG A:CYS39 3.8 0.0 1.0 CB A:THR19 3.9 0.0 1.0 O A:ALA18 4.1 98.4 1.0 ND2 A:ASN43 4.2 99.1 1.0 CG A:LYS40 4.2 97.7 1.0 O A:CYS39 4.3 95.5 1.0 C A:ALA18 4.4 96.6 1.0 CG2 A:THR19 4.5 99.8 1.0 CA A:LYS40 4.5 96.2 1.0 CB A:ALA18 4.7 95.0 1.0 N A:THR19 4.8 96.2 1.0 O A:MET36 4.8 95.1 1.0 CA A:THR19 4.9 98.6 1.0 N A:CYS39 4.9 94.4 1.0 CB A:LYS40 5.0 95.7 1.0

Mercury binding site 7 out of 8 in the Crystal Structure of the Ribosomal Protein L11-Rna Complex


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 7 of Crystal Structure of the Ribosomal Protein L11-Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg416 b:45.0 occ:0.10 N A:THR19 2.5 96.2 1.0 CG2 A:VAL24 2.6 91.8 1.0 CB A:VAL24 2.6 92.9 1.0 CG1 A:VAL24 2.9 90.9 1.0 CA A:THR19 2.9 98.6 1.0 SG A:CYS39 3.1 0.0 1.0 CG2 A:ILE35 3.5 87.7 1.0 C A:THR19 3.6 98.3 1.0 C A:ALA18 3.6 96.6 1.0 CB A:ALA18 3.9 95.0 1.0 CA A:ALA18 4.0 96.8 1.0 N A:GLY25 4.1 95.4 1.0 CA A:VAL24 4.1 96.0 1.0 N A:PRO20 4.1 0.0 1.0 O A:THR19 4.2 94.3 1.0 CB A:THR19 4.3 0.0 1.0 CD A:PRO20 4.4 0.0 1.0 O A:PRO20 4.5 0.0 1.0 CB A:CYS39 4.5 93.9 1.0 OG1 A:THR19 4.5 0.0 1.0 C A:VAL24 4.6 94.5 1.0 O A:ALA18 4.7 98.4 1.0 N A:VAL24 4.8 0.0 1.0 CA A:CYS39 4.9 95.6 1.0 CB A:ILE35 4.9 95.2 1.0

Mercury binding site 8 out of 8 in the Crystal Structure of the Ribosomal Protein L11-Rna Complex


Mono view


Stereo pair view

A full contact list of Mercury with other atoms in the Hg binding site number 8 of Crystal Structure of the Ribosomal Protein L11-Rna Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Hg448 b:21.0 occ:0.10 NE2 A:HIS31 2.1 84.8 1.0 O2 C:C1097 2.5 30.7 1.0 CE1 A:HIS31 2.5 81.3 1.0 CD2 A:HIS31 3.4 86.0 1.0 C2 C:C1097 3.5 31.3 1.0 ND1 A:HIS31 3.8 88.1 1.0 N3 C:C1097 3.9 27.5 1.0 CG A:HIS31 4.2 90.3 1.0 N1 C:A1096 4.5 19.5 1.0 N1 C:C1097 4.8 29.8 1.0 CG2 A:ILE9 4.8 74.1 1.0 C2 C:A1096 4.9 19.8 1.0

B.T.Wimberly, R.Guymon, J.P.Mccutcheon, S.W.White, V.Ramakrishnan. A Detailed View of A Ribosomal Active Site: the Structure of the L11-Rna Complex. Cell(Cambridge,Mass.) V. 97 491 1999.
ISSN: ISSN 0092-8674
PubMed: 10338213
DOI: 10.1016/S0092-8674(00)80759-X